microbetag : building a thorough database of genome-scale KO annotations
Description
In this repository we keep internal data for the microbetag microbial co-occurrence network annotator.
microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into.
As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file.
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gtdb_modelseed_gems.zip
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for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions |
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gtdb_kofam_scan_per_module.tar.gz
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all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. |
| updated_seedsets_of_interest.pckl |
A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC SeedSet |
| updated_non_seedsets_of_interest.pckl |
A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC NonSeedSet |
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phen_classes.zip
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A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome. |